Microbiology spectrum最新文献

{"title":"rRNA operon improves species-level classification of bacteria and microbial community analysis compared to 16S rRNA.","authors":"Sohyoung Won, Seoae Cho, Heebal Kim","doi":"10.1128/spectrum.00931-24","DOIUrl":"10.1128/spectrum.00931-24","url":null,"abstract":"<p><p>Precise identification of species is fundamental in microbial genomics and is crucial for understanding the microbial communities. While the 16S rRNA gene, particularly its V3-V4 regions, has been extensively employed for microbial identification, however has limitations in achieving species-level resolution. Advancements in long-read sequencing technologies have highlighted the rRNA operon as a more accurate marker for microbial classification and analysis than the 16S rRNA gene. This study aims to compare the accuracy of species classification and microbial community analysis using the rRNA operon versus the 16S rRNA gene. We evaluated the species classification accuracy of the rRNA operon,16S rRNA gene, and 16S rRNA V3-V4 regions using a BLAST-based method and a k-mer matching-based method with public data available from NCBI. We further performed simulations to model microbial community analysis. We accessed the performance using each marker in community composition estimation and differential abundance analysis. Our findings demonstrate that the rRNA operon offers an advantage over the 16S rRNA gene and its V3-V4 regions for species-level classification within the genus. When applied to microbial community analysis, the rRNA operon enables a more accurate determination of composition. Using the rRNA operon yielded more reliable results in differential abundance analysis as well.</p><p><strong>Importance: </strong>We quantitatively demonstrated that the rRNA operon outperformed the 16S rRNA and its V3-V4 regions in accuracy for both individual species identification and species-level microbial community analysis. Our findings can provide guidelines for selecting appropriate markers in the field of microbial research.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0093124"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537084/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142372336","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A drug repurposing screen identifies decitabine as an HSV-1 antiviral.","authors":"Laura Bautista, Cody Sirimanotham, Jason Espinoza, Dillon Cheng, Savaş Tay, Nir Drayman","doi":"10.1128/spectrum.01754-24","DOIUrl":"10.1128/spectrum.01754-24","url":null,"abstract":"<p><p>Herpes simplex virus type 1 (HSV-1) is a highly prevalent human pathogen that causes a range of clinical manifestations, including oral and genital herpes, keratitis, encephalitis, and disseminated neonatal disease. Despite its significant health and economic burden, there is currently only a handful of approved antiviral drugs to treat HSV-1 infection. Acyclovir and its analogs are the first-line treatment, but resistance often arises during prolonged treatment periods, such as in immunocompromised patients. Therefore, there is a critical need to identify novel antiviral agents against HSV-1. Here, we performed a drug repurposing screen, testing the ability of 1,900 safe-in-human drugs to inhibit HSV-1 infection <i>in vitro</i>. The screen identified decitabine, a cytidine analog that is used to treat myelodysplastic syndromes and acute myeloid leukemia, as a potent anti-HSV-1 agent. We show that decitabine is effective in inhibiting HSV-1 infection in multiple cell types, including human keratinocytes, that it synergizes with acyclovir, and acyclovir-resistant HSV-1 is still sensitive to decitabine. We further show that decitabine causes G > C and C > G transversions across the viral genome, suggesting it exerts its antiviral activity by lethal mutagenesis, although a role for decitabine's known targets, DNA methyl-transferases, has not been ruled out.</p><p><strong>Importance: </strong>Herpes simplex virus type 1 (HSV-1) is a prevalent human pathogen with a limited arsenal of antiviral agents, resistance to which can often develop during prolonged treatment, such as in the case of immunocompromised individuals. Development of novel antiviral agents is a costly and prolonged process, making new antivirals few and far between. Here, we employed an approach called drug repurposing to investigate the potential anti-HSV-1 activity of drugs that are known to be safe in humans, shortening the process of drug development considerably. We identified a nucleoside analog named decitabine as a potent anti-HSV-1 agent in cell culture and investigated its mechanism of action. Decitabine synergizes with the current anti herpetic acyclovir and increases the rate of mutations in the viral genome. Thus, decitabine is an attractive candidate for future studies in animal models to inform its possible application as a novel HSV-1 therapy.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0175424"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537057/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142291314","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of pKPN945B, a novel transferable IncR plasmid from hypervirulent carbapenem-resistant <i>Klebsiella pneumoniae</i>, harboring <i>bla</i>_IMP-4 and <i>qnrS1</i>.","authors":"Xue Xiao, Chunlin Feng, Jingchen Hao, Ling Cheng, Chunxia Jian, Zhangrui Zeng, Jinbo Liu","doi":"10.1128/spectrum.00491-24","DOIUrl":"10.1128/spectrum.00491-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Carbapenem-resistant &lt;i&gt;Klebsiella pneumoniae&lt;/i&gt; producing metallo-β-lactamase poses a major public health threat worldwide. Imipenemase often coexists with other resistance genes leading to the formation of multidrug-resistant bacteria. In this study, we describe the microbiological and genomic characteristics of the hypervirulent carbapenem-resistant &lt;i&gt;K. pneumoniae&lt;/i&gt; ST20-K23 strain KPN945 harboring &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;IMP-4&lt;/sub&gt; and &lt;i&gt;qnrS1&lt;/i&gt;. The minimum inhibitory concentration of KPN945 against antimicrobials was determined by the broth microdilution method. The virulence of KPN945 was evaluated through string test, serum killing resistance, and &lt;i&gt;Galleria mellonella&lt;/i&gt; larvae infection models. The transferability of pKPN945B was assessed using a conjugation test. The genome sequence characteristics of KPN945 were analyzed through whole genome sequencing, and a phylogenetic tree was constructed to evaluate the prevalence of imipenemase. Our findings showed that KPN945 was non-susceptible to β-lactam antibiotics, highly resistant to serum killing, and highly lethal to &lt;i&gt;G. mellonella&lt;/i&gt; larvae. The fusion plasmid pKPN945B carried by the isolate KPN945 belonged to the IncR incompatibility group and harbored multiple drug resistance genes such as &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;IMP-4&lt;/sub&gt;, &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;CTX-M-14&lt;/sub&gt;, &lt;i&gt;qnrS1&lt;/i&gt;, and &lt;i&gt;sul2&lt;/i&gt;. The most important point is that the IncR plasmid is a novel plasmid that arose by the accretion of parts from different plasmids, making it transferable and with a fitness cost. Globally, &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;IMP-4&lt;/sub&gt; is the most prevalent imipenemase subtype, with the highest isolation rates in Asia, particularly China. The spread of &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;IMP-4&lt;/sub&gt;, especially the emergence of transferable plasmids, deserves our vigilance and prevention. Additionally, we should pay attention to the formation of hypervirulent &lt;i&gt;K. pneumoniae&lt;/i&gt; mediated by non-virulent plasmids.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Up to now, IncR replicons carrying &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;IMP-4&lt;/sub&gt; have not been reported, and the IncR plasmids described in previous studies have been found to be non-transferrable to other bacteria through conjugation. Moreover, there have been no extensive phylogenetic analyses of strains carrying blaIMP in the published papers. The lack of data in these studies is noteworthy because blaIMP appears in the novel transferable fusion plasmid IncR. Although the IncR plasmid has no tra operon, it can still be transferred to &lt;i&gt;Escherichia coli&lt;/i&gt; EC600 or &lt;i&gt;Klebsiella&lt;/i&gt; pneumoniae ATCC13883 (RIF&lt;sup&gt;R&lt;/sup&gt;) without high fitness cost, but it only affects the MIC of imipenem. &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;IMP&lt;/sub&gt; integrates with other resistance mechanisms leading to the formation of multidrug-resistant strains. Notably, the high prevalence of &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;IMP-4&lt;/sub&gt; in Asia and the presence of &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;IMP-4&lt;/sub&gt; on novel transferable IncR plasmids suggest the urgent need to monitor the emergence of ","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0049124"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537061/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142291332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Wastewater-based intestinal protozoa monitoring in Shanghai, China.","authors":"Yanyan Jiang, Zhongying Yuan, Yaxue Wang, Jing Zhang, Yujuan Shen, Jianping Cao","doi":"10.1128/spectrum.04032-23","DOIUrl":"10.1128/spectrum.04032-23","url":null,"abstract":"<p><p>Intestinal protozoa <i>Cryptosporidium</i> spp., <i>Giardia duodenalis</i>, and <i>Enterocytozoon bieneusi</i> have been implicated in serious waterborne outbreaks worldwide. Wastewater-based epidemiology (WBE) is a promising approach for evaluating the disease prevalence in a catchment population in that it monitors the contamination level of the intestinal pathogens in wastewater. We collected 48 urban wastewater samples (24 from influents and 24 from effluents) from the Yangpu Wastewater Treatment Plant (YPWTP) in Shanghai, China. We identified <i>Cryptosporidium</i> spp., <i>G. duodenalis</i>, and <i>E. bieneusi</i> by nested polymerase chain reaction (PCR) amplification. <i>Cryptosporidium hominis</i> and subtype IdA14 were identified in two samples by analyzing the sequences of small subunit ribosomal RNA (SSU rRNA) and 60-kDa glycoprotein (<i>gp60</i>) genes, respectively. The <i>G. duodenalis</i> sub-assemblage AII (<i>n</i> = 8) and assemblage C (<i>n</i> = 4) in 12 samples were determined by analyzing triosephosphate isomerase (<i>tpi</i>) gene sequences. The <i>E. bieneusi</i> genotype A was identified in one sample by analyzing the sequence of the internal transcribed spacer (ITS) region of the rRNA gene. These findings suggest that improving wastewater treatment and monitoring the virility of pathogens in effluents is critical. We observed similar prevalence and genotypes/subtypes of the three intestinal protozoa in our wastewater samples as those reported in previous studies, providing evidence that WBE can be used as an effective epidemic management tool.IMPORTANCE<i>Cryptosporidium</i> spp., <i>Giardia duodenalis,</i> and <i>Enterocytozoon bieneusi</i> are common intestinal protozoa causing diarrhea. The infective oocysts, cysts, and spores released in feces can survive in different environments, including multiple types of water bodies. Humans can acquire these intestinal protozoan infections <i>via</i> the fecal-oral route as in waterborne transmission. Wastewater-based epidemiology can rapidly and reliably detect and monitor the emergence and spread of waterborne diseases. We detected <i>Cryptosporidium</i> spp., <i>G. duodenalis,</i> and <i>E. bieneusi</i> in a wastewater treatment plant in Shanghai, China, reflecting the occurrence and genetic characterizations of the three intestinal pathogens from community members served by the wastewater treatment plant.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0403223"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11540151/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142308054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Micronutrient availability alters <i>Candida albicans</i> growth and farnesol accumulation: implications for studies using RPMI-1640.","authors":"Cory H T Boone, Daniel J Gutzmann, Jaxon J Kramer, Shyanne D Urbin, Dhammika H Navarathna, Audrey L Atkin, Kenneth W Nickerson","doi":"10.1128/spectrum.01571-24","DOIUrl":"10.1128/spectrum.01571-24","url":null,"abstract":"<p><p>Science is challenging because we do not know what we do not know. Commercial chemicals are often marketed with >99% purity, but 0.5-1% impurity can impact results and cloud data interpretation. We recently developed an assay for farnesol and aromatic fusel alcohols from <i>Candida albicans</i>. During proof-of-concept experiments using RPMI-1640 growth media, the buffering compound was switched from MOPS obtained from Acros Organics to MOPS obtained from Sigma-Aldrich, both labeled 99% + purity. We observed a twofold decrease in growth, along with a three- to fivefold increase in farnesol production per cell upon the switch. ICP-MS showed that trace Mn(II) was present in Acros MOPS but absent in Sigma MOPS. Optimal growth was achieved by the addition of Mn(II), Zn(II), and Fe(II). We established upper and lower limits for Fe(II), Zn(II), Cu(II), and Mn(II) that allowed similar growth and then assessed 16 different mineral combinations in RPMI-1640 base media. The results show an increased production of farnesol and the aromatic fusel alcohols when Zn(II) is abundant, and a further increase in the aromatic fusel alcohols when both Fe(II) and Zn(II) are abundant. Finally, antifungal susceptibility testing displayed no significant difference between RPMI/MOPS with and without mineral supplementation. Supplemental Mn(II) was most needed for cell growth, while supplemental Zn(II) was most needed for the production of farnesol and the aromatic fusel alcohols. To avoid these artifacts due to metal contamination, we now use a modified RPMI supplemented with 1 mg/ L of Cu(II), Zn(II), Mn(II), and Fe(II).</p><p><strong>Importance: </strong>The dimorphic fungus <i>Candida albicans</i> is a major opportunistic pathogen of humans. RPMI-1640 is a chemically defined growth medium commonly used with <i>C. albicans</i>. We identified over 32,000 publications with keywords RPMI and <i>C. albicans</i>. Additionally, Antifungal Susceptibility Testing (AFST) protocols in the United States (CLSI) and Europe (EUCAST) utilize RPMI as a base media to assess drug efficacy against clinical fungal isolates. RPMI contains many nutrients but no added trace metals. We found that the growth characteristics with RPMI were dependent on which MOPS buffer was chosen and the contamination of that buffer by trace levels of Mn(II) and Zn(II). Added Mn(II) was most needed for cell growth while added Zn(II) was most needed for secretion of farnesol and other signaling molecules.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0157124"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537104/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142308146","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Role of rectal colonization by third-generation cephalosporin-resistant Enterobacterales on the risk of surgical site infection after hepato-pancreato-biliary surgery.","authors":"Miguel Rodríguez-Fernández, Marta Trigo-Rodríguez, Darío Martínez-Baena, Rocío Herrero, Reinaldo Espíndola-Gómez, Pedro Martínez Pérez-Crespo, Alberto Gallego Vela, Eva Torres, Ana Isabel Aller García, Eva M León, Juan E Corzo-Delgado, Pablo Parra-Membrives, Nicolás Merchante","doi":"10.1128/spectrum.00878-24","DOIUrl":"10.1128/spectrum.00878-24","url":null,"abstract":"<p><p>The impact of third-generation cephalosporin-resistant Enterobacterales (3GCR-E) rectal colonization in the development of subsequent infection after surgery is controversial. In particular, there is a lack of data in the context of hepato-pancreato-biliary (HPB) surgery. The objective of this study was to assess the prevalence of 3GCR-E intestinal carriage among patients undergoing elective HPB resection surgery and its impact on the incidence and etiology of surgical site infections (SSIs). This retrospective cohort study (January 2016-December 2022) was performed at Valme University Hospital (Seville, Spain). The inclusion criteria included (i) 18 years of age or older, (ii) undergoing elective HPB resection surgery, and (iii) availability of a periprocedural surveillance rectal swab culture to detect 3GCR-E. The prevalence of 3GCR-E intestinal carriage at elective HPB resection surgery was assessed, as well as SSI incidence at 30 days and possible associated factors. Two hundred nine patients were included. Eleven (5.3%) patients were colonized by 3GCR-E at baseline. According to 3GCR-E carriage status, 6 (55%) of the carriers developed SSI, whereas this occurred in 50 (25%) of non-carriers (<i>P</i> = 0.033). Likewise, the rates of SSI caused specifically by 3GCR-E were 83% (5 of 6) in 3GCR-E carriers and 6% (3 of 50) in non-carriers (<i>P</i> < 0.001). After multivariate analyses, 3GCR-E colonization at the time of surgery was identified as an independent predictor for developing SSI (adjusted odds ratio 4.63, 95% confidence interval: 1.177-18.232, <i>P</i> = 0.028). Despite a low prevalence of 3GCR-E intestinal carriage at surgery, 3GCR-E rectal colonization is associated with a higher risk of SSI among patients undergoing elective HPB resection surgery, with most SSIs being caused by the colonizing bacteria.</p><p><strong>Importance: </strong>In this Spanish retrospective cohort study, previous 3GCR-E rectal colonization was associated with a higher risk of SSI after hepato-pancreato-biliary resection surgeries. Most of SSIs were caused by the colonizing bacteria, suggesting a rationale for adapted perioperative antibiotic prophylaxis in known 3GCR-E colonized patients.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0087824"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537004/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142308149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Polymicrobial methicillin-resistant <i>Staphylococcus aureus</i> bloodstream infections.","authors":"Angelica Escalona, Emi Hayashi, Michelle Evans, Harm van Bakel, Bremy Alburquerque, Amy C Dupper, Russell McBride, Deena R Altman","doi":"10.1128/spectrum.01081-24","DOIUrl":"10.1128/spectrum.01081-24","url":null,"abstract":"<p><p>Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) bloodstream infection (BSI) is a serious public health concern. At times, MRSA is isolated from the blood along with other pathogens, the significance and consequences of which are not well described. This study aims to outline the clinical characteristics and outcomes of those with polymicrobial MRSA BSI compared with those with monomicrobial MRSA BSI. We conducted a retrospective case-control study of those with and without polymicrobial MRSA BSI from 2014 to 2022 at a single quaternary care center in New York City. Risk factors and outcomes for polymicrobial MRSA BSI were assessed using logistic regression analyses. Of 559 patients with MRSA BSI during the study period, 49 (9%) had polymicrobial MRSA BSI. Gram-positive <i>Enterococcus</i> (23%) was the most common co-pathogen. The presence of urinary (<i>P</i> = 0.02) and gastrointestinal (<i>P</i> < 0.01) devices was significantly associated with polymicrobial MRSA BSI. Polymicrobial MRSA BSI was associated with intensive care unit (ICU) admission after BSI (<i>P</i> = 0.01). Mortality did not differ. While polymicrobial MRSA BSI is relatively uncommon, it complicates an already complex clinical scenario of MRSA BSI.IMPORTANCE<i>Staphylococcus aureus</i> is a common human pathogen associated with severe disease and high mortality rates. Although clinically observed, little is known about the impact of polymicrobial staphylococcal bloodstream infection. This study evaluates polymicrobial methicillin-resistant <i>S. aureus</i> bloodstream infection (BSI), highlighting the increased risk of intensive care unit admission and impact on morbidity. Identifying risk factors for polymicrobial BSI, such as the presence of specific devices, can aid in early recognition and targeted interventions. Clarifying the risks and outcomes of polymicrobial infections can lead to strategies to minimize and manage these infections and explore the potential interactions between pathogens.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0108124"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11540167/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142350146","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparison of a hepatitis C core antigen assay to nucleic acid amplification testing for detection of hepatitis C viremia in a US population.","authors":"Ian L Gunsolus, John Prostko, Sandra Pearce, Biniam Degaga, Scott Eickstead, Russ Taylor, Jessica Grieshaber, Kyle Richard, Anne Hoffman, Aneta Pekalska, David Daghfal","doi":"10.1128/spectrum.00975-24","DOIUrl":"10.1128/spectrum.00975-24","url":null,"abstract":"<p><p>The prevalence of hepatitis C virus (HCV) infection in the United States has increased over the past decade despite the development of effective direct-acting antiviral treatments. To meet the World Health Organization's (WHO) goal of eliminating HCV infection by 2030, transmission events must be reduced. Currently, infection screening relies on detection of HCV antibodies, with nucleic acid amplification testing (NAAT) used to confirm HCV viremia and monitor changes in viral load. However, the seroconversion window for detection of HCV antibodies is long, averaging 6 weeks, with delayed seroconversion common in co-infected and immunosuppressed populations. Testing for HCV core antigen, which is present approximately 5 weeks before HCV antibodies, holds promise for earlier detection of HCV infection. It may also hold promise as a cheaper, more accessible, and more rapid alternative to NAAT for infection confirmation. Here, we evaluated the agreement between a research-use HCV Core Antigen Assay and NAAT among US patients receiving clinically indicated NAAT. Among 412 specimens, the overall concordance was 97.1%, with a positive percent agreement of 95.5%. Discrepancies primarily occurred among patients with chronic HCV and low viral loads; 11/12 discrepancies showed viral loads <4,000 IU/mL. Among patients being screened for HCV infection (i.e., excluding those undergoing NAAT for serial monitoring of a previously diagnosed infection), the positive percent agreement was 97.0%. Among patients undergoing serial testing, changes in HCV Core Antigen Assay signal-to-cut-off values were generally correlated with changes in the viral load. Results suggest that the research-use HCV Core Antigen Assay studied here may reliably detect and/or confirm HCV infection.</p><p><strong>Importance: </strong>A research-use HCV Core Antigen Assay showed high concordance with nucleic acid amplification testing for the detection of current hepatitis C infection. The assay may enable more rapid and lower-cost detection and/or confirmation of hepatitis C infection.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0097524"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537050/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142391738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the causes of variability in quality of oropharyngeal swab sampling for SARS-CoV-2 nucleic acid testing and proposed improvement measures: a multicenter, double-blind study.","authors":"Jie Zhu, Fanfan Xing, Yunzhu Li, Chunchen Wu, Shasha Li, Qin Wang, Jinyue Huang, Yafei Zhang, Xiaowei Zheng, Zhenjun Liu, Jianguo Rao, Rui Hong, Shuilin Tian, Shuangyun Xiong, Lin Tan, Xinlei Chen, Yanwu Li, Wei He, Xiaodan Hong, Jianbo Xia, Qiang Zhou, Zhenhua Zhang","doi":"10.1128/spectrum.01567-24","DOIUrl":"10.1128/spectrum.01567-24","url":null,"abstract":"<p><p>Although coronavirus disease 2019 (COVID-19) has not been considered a public health emergency of international concern since last year, intermittent regional impacts still persist, and accurate testing remains crucial. Ribonuclease <i>P</i> protein subunit P30 (<i>RPP30</i>) RNA, known for its broad and stable expression in tissue cells, was used to evaluate samples from 10 hospitals with over 3,000 negative nucleic acid tests. The results revealed that the overall pass rate for the collected samples was consistently low and exhibited significant heterogeneity. After reassessing the evaluative effectiveness of <i>RPP30</i> RNA Ct values from the samples of 132 positive individuals under quarantine observation, it was used to identify factors affecting sampling quality. These factors included different stages ranging from sample collection to PCR processing, various characteristics of both samplers and individuals being sampled, as well as sampling season and location. The results indicated that post-sampling handling had minimal impact, winter and fever clinic samples showed higher quality, whereas children's samples had lower quality. The key finding was that the characteristics of samplers were closely related to sampling quality, emphasizing the role of subjectivity. Quality control warnings led to substantial improvements, confirming this finding. Consequently, although there are various factors during the testing process, the most critical aspect is to improve, supervise, and maintain standardized practices among sampling staff.<b>IMPORTANCE</b>This study further confirmed the reliability of internal references (IRs) in assessing sample quality, and utilized a large sample IR data to comprehensively and multidimensionally identify significant interference factors in nucleic acid test results. By further reminding and intervening in the subjective practices of specimen collectors, good results could be achieved.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0156724"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537049/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142391743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamic microbiome diversity shaping the adaptation of sponge holobionts in coastal waters.","authors":"Bifu Gan, Kai Wang, Beibei Zhang, Chenzheng Jia, Xin Lin, Jing Zhao, Shaoxiong Ding","doi":"10.1128/spectrum.01448-24","DOIUrl":"10.1128/spectrum.01448-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The microbial communities associated with sponges contribute to the adaptation of hosts to environments, which are essential for the trophic transformation of benthic-marine coupling. However, little is known about the symbiotic microbial community interactions and adaptative strategies of high- and low-microbial abundance (HMA and LMA) sponges, which represent two typical ecological phenotypes. Here, we compared the 1-year dynamic patterns of microbiomes with the HMA sponge &lt;i&gt;Spongia officinalis&lt;/i&gt; and two LMA sponge species &lt;i&gt;Tedania&lt;/i&gt; sp. and &lt;i&gt;Haliclona simulans&lt;/i&gt; widespread on the coast of China. Symbiotic bacterial communities with the characteristic HMA-LMA dichotomy presented higher diversity and stability in &lt;i&gt;S. officinalis&lt;/i&gt; than in &lt;i&gt;Tedania&lt;/i&gt; sp. and &lt;i&gt;H. simulans&lt;/i&gt;, while archaeal communities showed consistent diversity across all sponges throughout the year. Dissolved oxygen, dissolved inorganic phosphorus, dissolved organic phosphorus, and especially temperature were the major factors affecting the seasonal changes in sponge microbial communities. &lt;i&gt;S. officinalis&lt;/i&gt;-associated microbiome had higher diversity, stronger stability, and closer interaction, which adopted a relatively isolated strategy to cope with environmental changes, while &lt;i&gt;Tedania&lt;/i&gt; sp. and &lt;i&gt;H. simulans&lt;/i&gt; were more susceptible and shared more bacterial Amplicon Sequence Variants (ASVs) with surrounding waters, with an open way facing the uncertainty of the environment. Meta-analysis of the microbiome in composition, diversity, and ecological function from 13 marine sponges further supported that bacterial communities associated with HMA and LMA sponges have evolved two distinct environmental adaptation strategies. We propose that the different adaptive ways of sponges responding to the environment may be responsible for their successful evolution and their competence in global ocean change.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;During long-term evolution, sponge holobionts, among the oldest symbiotic relationships between microbes and metazoans, developed two distinct phenotypes with high- and low-microbial abundance (HMA and LMA). Despite sporadic studies indicating that the characteristic microbial assemblages present in HMA and LMA sponges, the adaptation strategies of symbionts responding to environments are still unclear. This deficiency limits our understanding of the selection of symbionts and the ecological functions during the evolutionary history and the adaptative assessment of HMA and LMA sponges in variable environments. Here, we explored symbiotic communities with two distinct phenotypes in a 1-year dynamic environment and combined with the meta-analysis of 13 sponges. The different strategies of symbionts in adapting to the environment were basically drawn: microbes with LMA were more acclimated to environmental changes, forming relatively loose-connected communities, while HMA developed relatively tight-connected and m","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0144824"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537060/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}